[2024-01-24 12:42:06,029] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:06,030] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:06,030] [INFO] DQC Reference Directory: /var/lib/cwl/stg450c56bd-4f4e-4f52-a86a-a56ba06729f6/dqc_reference
[2024-01-24 12:42:07,246] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:07,247] [INFO] Task started: Prodigal
[2024-01-24 12:42:07,247] [INFO] Running command: gunzip -c /var/lib/cwl/stgf85456c6-3a2a-4fae-883a-94537b802b30/GCF_000831645.3_ASM83164v3_genomic.fna.gz | prodigal -d GCF_000831645.3_ASM83164v3_genomic.fna/cds.fna -a GCF_000831645.3_ASM83164v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:13,444] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:13,444] [INFO] Task started: HMMsearch
[2024-01-24 12:42:13,445] [INFO] Running command: hmmsearch --tblout GCF_000831645.3_ASM83164v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg450c56bd-4f4e-4f52-a86a-a56ba06729f6/dqc_reference/reference_markers.hmm GCF_000831645.3_ASM83164v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:13,687] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:13,689] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf85456c6-3a2a-4fae-883a-94537b802b30/GCF_000831645.3_ASM83164v3_genomic.fna.gz]
[2024-01-24 12:42:13,715] [INFO] Query marker FASTA was written to GCF_000831645.3_ASM83164v3_genomic.fna/markers.fasta
[2024-01-24 12:42:13,715] [INFO] Task started: Blastn
[2024-01-24 12:42:13,715] [INFO] Running command: blastn -query GCF_000831645.3_ASM83164v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg450c56bd-4f4e-4f52-a86a-a56ba06729f6/dqc_reference/reference_markers.fasta -out GCF_000831645.3_ASM83164v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:14,293] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:14,297] [INFO] Selected 11 target genomes.
[2024-01-24 12:42:14,297] [INFO] Target genome list was writen to GCF_000831645.3_ASM83164v3_genomic.fna/target_genomes.txt
[2024-01-24 12:42:14,318] [INFO] Task started: fastANI
[2024-01-24 12:42:14,318] [INFO] Running command: fastANI --query /var/lib/cwl/stgf85456c6-3a2a-4fae-883a-94537b802b30/GCF_000831645.3_ASM83164v3_genomic.fna.gz --refList GCF_000831645.3_ASM83164v3_genomic.fna/target_genomes.txt --output GCF_000831645.3_ASM83164v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:28,128] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:28,129] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg450c56bd-4f4e-4f52-a86a-a56ba06729f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:28,129] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg450c56bd-4f4e-4f52-a86a-a56ba06729f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:28,140] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:42:28,140] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:42:28,140] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Companilactobacillus heilongjiangensis	strain=DSM 28069	GCA_000831645.3	1074467	1074467	type	True	100.0	930	930	95	conclusive
Companilactobacillus heilongjiangensis	strain=S4-3	GCA_005405325.1	1074467	1074467	type	True	99.9624	896	930	95	conclusive
Companilactobacillus huachuanensis	strain=395-6.2	GCA_005404815.1	2559914	2559914	type	True	87.3601	743	930	95	below_threshold
Companilactobacillus nantensis	strain=DSM 16982	GCA_001435815.1	305793	305793	type	True	84.9464	657	930	95	below_threshold
Companilactobacillus zhachilii	strain=HBUAS52074	GCA_003606365.2	2304606	2304606	type	True	84.5883	629	930	95	below_threshold
Companilactobacillus musae	strain=313	GCA_003573575.1	1903258	1903258	type	True	82.7598	494	930	95	below_threshold
Companilactobacillus kimchii	strain=DSM 13961	GCA_009764365.1	2801452	2801452	type	True	81.6292	434	930	95	below_threshold
Companilactobacillus paralimentarius	strain=DSM 13238	GCA_009764345.1	83526	83526	type	True	81.5722	404	930	95	below_threshold
Companilactobacillus allii	strain=WiKim39	GCA_023923085.1	1847728	1847728	type	True	79.7761	255	930	95	below_threshold
Companilactobacillus mishanensis	strain=256-3	GCA_003946505.1	2486008	2486008	type	True	78.8664	204	930	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:28,142] [INFO] DFAST Taxonomy check result was written to GCF_000831645.3_ASM83164v3_genomic.fna/tc_result.tsv
[2024-01-24 12:42:28,143] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:28,143] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:28,143] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg450c56bd-4f4e-4f52-a86a-a56ba06729f6/dqc_reference/checkm_data
[2024-01-24 12:42:28,145] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:28,174] [INFO] Task started: CheckM
[2024-01-24 12:42:28,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000831645.3_ASM83164v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000831645.3_ASM83164v3_genomic.fna/checkm_input GCF_000831645.3_ASM83164v3_genomic.fna/checkm_result
[2024-01-24 12:42:53,471] [INFO] Task succeeded: CheckM
[2024-01-24 12:42:53,472] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:42:53,495] [INFO] ===== Completeness check finished =====
[2024-01-24 12:42:53,496] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:42:53,496] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000831645.3_ASM83164v3_genomic.fna/markers.fasta)
[2024-01-24 12:42:53,497] [INFO] Task started: Blastn
[2024-01-24 12:42:53,497] [INFO] Running command: blastn -query GCF_000831645.3_ASM83164v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg450c56bd-4f4e-4f52-a86a-a56ba06729f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000831645.3_ASM83164v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:54,265] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:54,269] [INFO] Selected 7 target genomes.
[2024-01-24 12:42:54,269] [INFO] Target genome list was writen to GCF_000831645.3_ASM83164v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:42:54,280] [INFO] Task started: fastANI
[2024-01-24 12:42:54,281] [INFO] Running command: fastANI --query /var/lib/cwl/stgf85456c6-3a2a-4fae-883a-94537b802b30/GCF_000831645.3_ASM83164v3_genomic.fna.gz --refList GCF_000831645.3_ASM83164v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000831645.3_ASM83164v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:43:04,853] [INFO] Task succeeded: fastANI
[2024-01-24 12:43:04,866] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:43:04,867] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000831645.3	s__Companilactobacillus heilongjiangensis	100.0	929	930	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_005404815.1	s__Companilactobacillus huachuanensis	87.3227	744	930	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435815.1	s__Companilactobacillus nantensis	84.8967	661	930	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003606365.2	s__Companilactobacillus zhachilii	84.6615	626	930	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	97.75	97.75	0.87	0.87	2	-
GCF_003967595.1	s__Companilactobacillus musae	82.7202	485	930	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001434275.1	s__Companilactobacillus mindensis	82.5877	452	930	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001435445.1	s__Companilactobacillus kimchii	81.4309	439	930	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.99	99.97	1.00	1.00	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:43:04,868] [INFO] GTDB search result was written to GCF_000831645.3_ASM83164v3_genomic.fna/result_gtdb.tsv
[2024-01-24 12:43:04,869] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:43:04,872] [INFO] DFAST_QC result json was written to GCF_000831645.3_ASM83164v3_genomic.fna/dqc_result.json
[2024-01-24 12:43:04,872] [INFO] DFAST_QC completed!
[2024-01-24 12:43:04,872] [INFO] Total running time: 0h0m59s